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Applying phylogenies to practical issues in SE Asia: data, methods, and speculation

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Title: Applying phylogenies to practical issues in SE Asia: data, methods, and speculation


1
Applying phylogenies to practical issues in SE
Asia data, methods, and speculation Chuck
Cannon Texas Tech University
2
The first great extinction wilderness
3
Research
  • Ecoregional Conservation Assessment of Sulawesi
  • (The Nature Conservancy Indonesia)
  • Phylogeographic survey of SE Asian stone oaks
  • Reconstruction of biogeographic history of
    Southeast Asian rainforest
  • DNA fingerprinting of tropical timbers
  • Genomic signatures from DNA microarrays

4
SE Asia
Two major biogeographic boundaries Megadiverse
forests Complex historical setting Strong
ecological gradients Human activity causing rapid
changes
5
Ecoregional Conservation Assessment of
Sulawesi Data 32 satellite images Digital
elevation model Soil types Collection
records Four week rapid survey
J.R. Harting, Agus Salim and Marcy Summers
Forest type map shown
6
Ecoregional Conservation Assessment of
Sulawesi Condition A fairly large amount of good
forest left Vulnerable forests adjacent to old
growth
Forest condition map shown
7
Ecoregional Conservation Assessment of Sulawesi
The real object of this exercise was to
prioritize and develop a conservation
portfolio. What good is a phylogeny in this
situation? Could insight into phylodiversity
influence the development of a conservation
portfolio? What measure of phylodiversity is most
accurate and relevant?
8
Ecoregional Conservation Assessment of Sulawesi
Using georeferenced collection database and green
plant supertree to evaluate the phylodiversity of
each forest type Various types of phylodiversity
measures Whole tree diversity Endemic parts of
tree Ecologically critical parts of tree
9
Ecoregional Conservation Assessment of Sulawesi
  • An example of poor data
  • Collection records heavily biased
  • Supertree not adequately resolved/not relevant to
    local diversity
  • A very useful exercise and an important input to
    the decision process

10
SE Asian stone oaks
P.S. Manos, S-H Oh
Lithocarpus Fagaceae Good model system Fruits
acorn-like, greater diversity than temperate
oaks Generalized insect pollination
11
SE Asian stone oaks
Intergenic cpDNA sequence (1 locus, 659 bp) 381
individuals, 4 genera, 13 sections, 79 species,
and 12 locations
12
stone oaks
381 individuals, 4 genera, 13 sections, 79
species, and 12 locations
Diameter of circle indicates abundance White
circles are shared among locations (density map
shown inside) Solid color circles are
endemic Black squares are missing types
This map represents collection effort in each
location
13
stone oaks
Two main clades A1 ancestral, most abundant,
most widespread, most taxonomically
diverse Strong geographic structure Elevation
gradient in Sundaland clade No obvious pattern in
fruit type Castanopsis shares A1 No monophyletic
species
14
stone oaks
Each location has a distinct pattern of
relatedness
Pairwise relatedness Hi Lo
15
SE Asian biogeographic model
Land area reconstructions Oligocene to early
Pliocene
16
SE Asia
17
SE Asian biogeographic model
Sea level affects land area and
fragmentation Temperature affects elevation
gradient
Bintanja et al. 2005
Habitat area reconstructions last million years
18
SE Asian melting pot
Geographic locations are as cohesive as
species. Many species are near equilibrium on the
network.
Location
Species
19
stone oaks species
20
SE Asian disequilibrium
Last Glacial Maximum 15,000 years ago Sea levels
down 120 m Temps down by 6C Climate probably
wet Lowland and Montane areas at a maximum
Current conditions Communities are diversity
concentrates 100-200 generations not enough
evolution Once allopatric, now sympatric Abundant
secondary contact Rare and endemic species
hybrid offspring?
21
Regional phylogeographic study of SE Asian stone
oaks
  • An example of okay data
  • DNA sequence data
  • Generic level sampling, including all important
    centers of diversity
  • Locus by locus approach frustrating in this
    genomic age (22 more years?!?!?)
  • Points to strong geographic structure of genetic
    variation in these forests, particularly in
    cytoplasmic genome

22
DNA fingerprinting of tropical timbers
  • Illegal logging and smuggling a huge problem in
    SE Asia
  • ITTO and international trade bodies searching for
    an objective third-party method to verify
    legality and sustainability
  • These approaches are used in human court cases
    and have been used to identify animal tissues in
    wild game trade
  • Biggest stumbling block is constructing adequate
    database

23
DNA fingerprinting of tropical timbers
  • Microsatellite studies of Shorea platyclados
  • MJ Asif, C-S Kua, R. Wickneswari, C-T Tan
  • six cross-amplified loci
  • Three locations 134 individuals

Hard and soft homoplasy prevent detailed
structure in these results
24
Genomic signatures
  • DNA microarrays?
  • 44K spots last year, 400K now, 1M soon?
  • Expensive! Single-use!
  • Use as upstream technique to harvest database
  • Cheap downstream assays
  • Design a custom array which does not require
    prior knowledge of genome and targets neutral
    variation

25
Genomic signatures
  • Hyperdispersed Illiterate Primer Screening
  • - Icoria, RTP (P. Hurban and E. Lobenhofer)
  • - Kua C-S
  • Anonymous 25mer probe sequences
  • H sequences are as unique as possible
  • I no open reading frame
  • P match optimal criteria for PCR primers
  • S whole genome

26
Genomic signatures
  • Hyperdispersed Illiterate Primer Screening
  • Proof of concept experiments
  • 3 known genomes and 1 unknown
  • (human, rat, mouse) (ramin)
  • All pairwise comparisons of knowns
  • Pairwise test of two different populations of
    unknown

27
Genomic signatures
28
Ramin
29
Genomic signatures in silico tests
BLAST results (1002 probes) Even distribution
across genome Reflects general rate of
nucleotide evolution (is dog supposed to be
faster?)
30
Genomic signatures
Including duplicate hits (28,383 hits) More
normal relationships Reflects general rate of
nucleotide evolution (is dog supposed to faster?)
31
Genomic signatures
32
Genomic signatures
33
Genomic signatures
in silico tests DONE LIST Blast chromosome
libraries of known genomes (nblast is too narrow
for this purpose) TO DO LIST Restrict
genomes Score complementarity for entire probe
sequence Correlate hyb intensity with target
position and complementarity Make predictions for
known genomes Refine probe design
34
Genomic signatures
Database of hybridization results
Phylogenetically scalable marker sets Virtual
genomic comparisons Query database and get back
most informative set of markers Easily 100s of
informative markers in each comparison
35
DNA fingerprinting of tropical timbers
  • Genomic signature database can be used to track
    timber, identify species
  • Downstream assays will be cheap and easy, ideally
    a simple presence/absence test
  • Allow producers to demonstrate their legality and
    shed stigma of corrupt 3rd world company
  • Allow buyers to objectively distinguish among
    shipments and their legality

36
Genomic signatures
  • Many more applications
  • clade mixture comparisons could help resolve
    tough nodes in supertree
  • Identification of evolutionarily important
    regions by performing comparisons between
    divergent morphologies
  • Much improved Barcode of Life
  • Etc

37
Thanks!
C-S Kua National Science Foundation P.S.
Manos National Geographic Society J.R.
Harting TTU Technological Transfer C.O. Webb TTU
Dept. of Biological Sciences W.B. Maynard The
Nature Conservancy P. Hurban Indonesian
government E.K. Lobenhofer Malaysian
government S-H Oh UNDP/GEF/FRIM Pahang peat swamp
project R. Wickneswari M.J. Asif C-T Tan K-S Lee
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